Conservation in mitochondrial DNA: Parallelized estimation and alignment influence

The wide availability of sequenced biological data has challenged the conventional methods and tools used in molecular biology to compute the conservation index. As the size of input datasets increases, the time-cost of current conservation methods is becoming unaffordable. We propose a new software tool that combines several estimation methods applied to the conservation computation process with parallelization and divide-and-conquer techniques substantially improving its performance without affecting its accuracy. We have also made an in-depth analysis of the impact of different methods and parameter selection on the alignment process applied to input datasets prior to their conservation analysis. We have used sets of mitochondrial DNA sequences with different levels of heterogeneity and length, to provide a full case study. Both the software tool and the input datasets used in this research are freely available at http://www.zaramit.orglconservation_index.